What is Protein Symmetry?

Many proteins interact with each other to form symmetrical assemblies. Participating proteins or subunits in such assemblies are related by symmetry operations.

The advantage of symmetrical assemblies is that they bring together multiple functional sites into close proximity for biological function; build large, functional shapes from many copies of a smaller protein subunit (they are economical to encode in the genome); and provide mechanisms for regulation of protein functions. The majority of symmetrical assemblies have perfect symmetry - i.e., all subunits have identical interactions with their neighbors. However, in some cases the subunits are related by apparent but not exact symmetry (called pseudosymmetry). The approximate symmetries may play a key role in their function - for example, similar (but not identical) subunits may form an assembly that interacts with a small molecule ligand and/or another protein. To learn more about types of symmetry present in PDB assemblies, see the Symmetry Resources in the PDB page.

Since symmetry is an essential feature of biomolecules, the RCSB provides information on the symmetries found within all complexes in the archive. This information is calculated and updated weekly. The RCSB also provides methods for finding structures and/or assemblies based on their symmetry.

Why use the Protein Symmetry Browser?

Oligomeric assemblies are stabilized by specific interactions. Exploring these interactions can provide insights into how an assembly is formed. In some cases, changes in the environment or inclusion of a small molecule or protein regulator can change the local and/or global assembly symmetries. Using this browser provides opportunities to examine protein assemblies that have similar symmetrical arrangements and explore interactions that lead to biological functions, cooperativity, and/or regulation.

How to use the Protein Symmetry Browser?

The Protein Symmetry Browser combines two different ways of organizing assemblies in the PDB - level of symmetry and type of symmetry operation.

• You can search for a specific type of point symmetry by its Schoenflies symbol (e.g., Cn, Dn, T, O, or I) or by helical symmetry H. Learn more about Schoenflies symbols.
• If you are looking for a specific level of symmetry - i.e., global symmetry, local symmetry, or pseudo symmetry, you can first search for the level of symmetry and then the symmetry operation of interest.

Once you have identified a level of symmetry and type of symmetry operation, you can view the associated polymer entities in the PDB and select the ones you wish to explore.

Examples

1. Browse through structures with global Cyclic symmetry (C5).

• Open the browse tree as follows: Global Symmetry >> Cyclic >> C5 >> Homo-5-mer
• The number listed next to the symmetry class (Homo-5-mer) indicates the number of assemblies that match the selected symmetry. Clicking on it will launch a search for all assemblies in the PDB that are associated with the level and type of symmetry.

2. Browse through structures with local Cyclic symmetry (C5).

• Open the browse tree as follows: Local Symmetry >> Cyclic >> C5 >> Homo-5-mer
• The number listed next to the symmetry class (Homo-5-mer) indicates the number of assemblies that match the selected symmetry. Clicking on it will launch a search for all assemblies in the PDB that are associated with the level and type of symmetry.

3. Browse through structures with pseudo Cyclic symmetry (C5).

• Open the browse tree as follows: Local Symmetry >> Cyclic >> C5 >> Homo-5-mer
• The number listed next to the symmetry class (Homo-5-mer) indicates the number of assemblies that match the selected symmetry. Clicking on it will launch a search for all assemblies in the PDB that are associated with the level and type of symmetry.